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6th Scientific School "Dynamics of Complex Networks and their Applications", DCNA 2022

作者： Nasybullin, Albert Maksimenko, Vladimir Kurkin, Semen Innopolis University Laboratory of Data Analysis and Bioinformatics Center for Artificial Intelligence Innopolis Russia Innopolis University Neuroscience and Cognitive Technology Laboratory Center for Technologies in Robotics and Mechatronics Components Innopolis Russia

ISBN: (数字)9781665461740

ISBN: (纸本)9781665461740

In this paper, we discuss a Machine Learning pipeline for the classification of EEG data. We propose a combination of synthetic data generation, long short-term memory artificial neural network (LSTM), and fine-tuning to solve classification problems for experiments with implicit visual stimuli, such as the Necker cube with different levels of ambiguity. The developed approach increased the quality of the classification model of raw EEG data. © 2022 IEEE.

关键词： Classification (of information)

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Clinical Informatics Approaches to Facilitate Cancer data Sharing

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Yearbook of Medical Informatics 2023年第1期32卷 104-110页

作者： Aneja, Sanjay Avesta, Arman Xu, Hua Machado, Lucila Ohno Department of Therapeutic Radiology Yale School of Medicine New Haven CT United States Center for Outcomes Research and Evaluation at Yale New Haven CT United States Department of Bioinformatics and Data Science Yale School of Medicine New Haven CT United States

OBJECTIVES: Despite growing enthusiasm surrounding the utility of clinical informatics to improve cancer outcomes, data availability remains a persistent bottleneck to progress. Difficulty combining data with protected health information often limits our ability to aggregate larger more representative datasets for analysis. With the rise of machine learning techniques that require increasing amounts of clinical data, these barriers have magnified. Here, we review recent efforts within clinical informatics to address issues related to safely sharing cancer data. METHODS: We carried out a narrative review of clinical informatics studies related to sharing protected health data within cancer studies published from 2018-2022, with a focus on domains such as decentralized analytics, homomorphic encryption, and common data models. RESULTS: Clinical informatics studies that investigated cancer data sharing were identified. A particular focus of the search yielded studies on decentralized analytics, homomorphic encryption, and common data models. Decentralized analytics has been prototyped across genomic, imaging, and clinical data with the most advances in diagnostic image analysis. Homomorphic encryption was most often employed on genomic data and less on imaging and clinical data. Common data models primarily involve clinical data from the electronic health record. Although all methods have robust research, there are limited studies showing wide scale implementation. CONCLUSIONS: Decentralized analytics, homomorphic encryption, and common data models represent promising solutions to improve cancer data sharing. Promising results thus far have been limited to smaller settings. Future studies should be focused on evaluating the scalability and efficacy of these methods across clinical settings of varying resources and expertise. IMIA and Thieme. This is an open access article published by Thieme under the terms of the Creative Commons Attribution-NonDerivative-NonCommercia

关键词： cancer common data models data sharing encryption federated learning

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Asymptotics of Bayesian Uncertainty Estimation in Random Features Regression 37

Asymptotics of Bayesian Uncertainty Estimation in Random Fea...

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37th Conference on Neural Information Processing Systems, NeurIPS 2023

作者： Baek, Youngsoo Berchuck, Samuel I. Mukherjee, Sayan Department of Statistical Science Duke University DurhamNC27705 United States Department of Biostatistics & Bioinformatics Duke University DurhamNC27705 United States Center for Scalable Data Analysis and Artificial Intelligence Universität Leipzig Leipzig04105 Germany Deparments of Mathematics Computer Science Biostatistics & Bioinformatics Duke University NC United States

ISBN: (纸本)9781713899921

In this paper, we compare and contrast the behavior of the posterior predictive distribution to the risk of the maximum a posteriori (MAP) estimator for the random features regression model in the overparameterized regime. We will focus on the variance of the posterior predictive distribution (Bayesian model average) and compare its asymptotics to that of the risk of the MAP estimator. In the regime where the model dimensions grow faster than any constant multiple of the number of samples, asymptotic agreement between these two quantities is governed by the phase transition in the signal-to-noise ratio. They also asymptotically agree with each other when the number of samples grows faster than any constant multiple of model dimensions. Numerical simulations illustrate finer distributional properties of the two quantities for finite dimensions. We conjecture they have Gaussian fluctuations and exhibit similar properties as found by previous authors in a Gaussian sequence model, which is of independent theoretical interest. © 2023 Neural information processing systems foundation. All rights reserved.

关键词： Signal to noise ratio

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Comparative Analysis of CNN Models for Multiclass Detection on Colon Disease 9

Comparative Analysis of CNN Models for Multiclass Detection ...

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9th International Conference on Information Technology and Digital Applications, ICITDA 2024

作者： Sulistyawan, Jason Sebastian Nugroho, Kuncahyo Setyo Isnan, Mahmud Pardamean, Bens Binus Graduate Program Bina Nusantara University Computer Science Department Jakarta11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia School of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9798331510732

Gastrointestinal diseases are significant health concerns that mostly affect the digestive and biliary tracts. These can only be observed internally through endoscopy, or a modern approach named Wireless Capsule Endoscopy. Though the approach has proven to work, the process relies heavily on medical experts, which is prone to error when given a considerably large load. The use of deep learning in detecting diseases with images has been proven to work in various cases and can be implemented for gastrointestinal diseases. This study compared four deep learning models based on Convolutional Neural Network architectures consisting of the VGG16, ResNet152V2, InceptionV3, and Xception for classifying colon disease images. The experiment showed that the ResNet152V2 performed the best, compared to the other three with a testing accuracy score of 0.9837. On the other hand, the VGG16 had the lowest performance with around accuracy score of 0.89 while the Xception and InceptionV3models yielded similar accuracy scores of 0.9587 and 0.9549, respectively. The results highlight the effectiveness of ResNet152V2 in handling the complexity of colon disease detection © 2024 IEEE.

关键词： Convolutional neural networks

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Automatic Multiple Choice Question Generation: A Systematic Literature Review 9

Automatic Multiple Choice Question Generation: A Systematic ...

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9th International Conference on Information Technology and Digital Applications, ICITDA 2024

作者： Henry, Matthew Martianus Heryanto, Nur Adhianti Isnan, Mahmud Nugroho, Kuncahyo Setyo Pardamean, Bens Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia School of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia Bina Nusantara University Binus Graduate Program Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9798331510732

Despite their drawbacks, multiple-choice questions (MCQ) have been widely used to assess the students' understanding of lectures through examinations. The development of automatic MCQ generation is beneficial, especially for educators. As a starting point for further development, a Systematic Literature Review (SLR) is conducted to uncover current trends, future challenges, and opportunities in automatic MCQ generation. Previously, an SLR was conducted, but it lacks coverage of the utilization of transformer-based models. This SLR covers the development of automatic MCQ generation using either traditional or advanced approaches such as Transformers. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses framework was used to gather the data from Scopus, IEEE Xplore, SpringerLink, arXiv, and Semantic Scholar. The included articles must be open-access computer science conference papers or journal articles and written in English less than five years ago. Four independent reviewers analyzed the research workflow, evaluation metric, and dataset used in each study. There are 18 included studies, where 17% (n = 3) studies are from 2024, 33% (n = 6) studies are from 2023, 22% (n = 4) studies are from 2022, 11% (n = 2) studies are from 2021, and 17% (n = 3) studies are from 2020. There are 33% (n = 6) of the studies used the traditional feature-based engineering approach, 39% (n = 7) of the studies used the Transformer-based model fine-tuning approach, and the remaining used novel approaches. The study found that BERT variants are the most utilized Transformer-based model in automatic MCQ. The research notes some challenges, but also open various opportunities for further research, including Large Language Model (LLM) utilization for automatic MCQ generation, the utilization BERT-based models for standardized machine-learned evaluation metrics, and the initiative for the creation of an MCQ dataset benchmark. © 2024 IEEE.

关键词： Semantics

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Automatic question generation for bahasa indonesia examination using copynet 9th

Automatic question generation for bahasa indonesia examinati...

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9th International Conference on Computer Science and Computational Intelligence, ICCSCI 2024

作者： Henry, Matthew Martianus Elwirehardja, Gregorius Natanael Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta11480 Indonesia

In educational institutions, an educator is responsible for assessing the student's knowledge grasp through examination. Creating exam questions, even the low-level factoid questions, is time-consuming, especially for inexperienced educators. Therefore, this study aims to create a sequence-to-sequence model using CopyNet by exploiting its copying mechanism advantage to automatically generate Bahasa Indonesia factoid questions to ease the educator's burden. Indonesian records in the TyDi QA dataset are used as the model input. GRU and Bi-GRU are employed as the CopyNet encoder, while LSTM is used as the CopyNet decoder. The model that utilizes GRU as the encoder achieves BLEU1, BLEU2, BLEU3, BLEU4, and ROUGE-L scores of 0.28, 0.19, 0.14, 0.1, and 0.32, respectively. Bi-GRU utilization as the model encoder achieves BLEU1, BLEU2, BLEU3, BLEU4, and ROUGE-L scores of 0.26, 0.17, 0.12, 0.09, and 0.30, respectively. Models using either encoder still achieve low scores. However, compared with the previous work, the result is still on par regarding the BLEU score. Further examination found that the generated questions do not adhere to semantic and syntactical correctness. Adding more records to the dataset and utilizing a more advanced architecture like CopyBERT are encouraged to improve the model performance in future work. Despite the result, this study has shown that CopyNet, primarily designed for text summarization or single-turn dialogue, can be tailored for factoid question generation. © 2024 The Authors.

关键词： Semantics

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Leveraging user-item interactions and hotel characteristics for hotel recommendations in Indonesia with graph neural networks

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Procedia Computer Science 2024年 245卷 710-719页

作者： Francis Alexander Panarto Tyrone Matthew Phanghegar Vincent Gunardi Tjeng Wawan Cenggoro Computer Science Department School of Computer Science Bina Nusantara University Jakarta 11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta 11480 Indonesia

Travelers usually check information about the destination before they decide to go. However, sometimes the information is too much to handle and causes confusion . A filtering mechanism is needed to help them make their choices . The solution is to implement a recommendation system; some common techniques that are used for this are Collaborative Filtering and content- based filtering, but both techniques have their flaws. Therefore, we propose a solution to combine those two methods through Graph Neural Network architectures to help fix their flaws . The proposed method will be used for recommending hotels in Indonesia using the HotelRec dataset as the base dataset and hotel features acquired from the TripAdvisor API. We use several GNN architectures, such as GCN, LightGCN, GraphSAGE, and GAT, to implement our approach. Then, we compare it to several baseline models, such as SVD and NeuMF, which are common baselines in recommendation systems. The performance of these models is calculated based on three metrics: HitRate@K, NDCG@K, and Recall@K. Based on the result of this experiment, we found that incorporating hotel features into the learning process of the model, accompanied by user-item interactions, boosted the model's performance by at least 20% in all metrics, especially in datasets with a smaller number of interactions.

关键词： Recommendation Systems Graph Neural Network Hotel Recommendation Collaborative Filtering Content -Based Indonesia

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bioinformatics exploration into potential mechanisms of Calamus draco for colorectal cancer treatment 9th

Bioinformatics exploration into potential mechanisms of Cala...

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9th International Conference on Computer Science and Computational Intelligence, ICCSCI 2024

作者： Kenneth, Christian Nirwantono, Rudi Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Biotechnology Department Faculty of Engineering Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Computer Science Program Bina Nusantara University Jakarta11480 Indonesia

As one of the cancer types with the highest incidence rates, colorectal cancer (CRC) would benefit from treatments with fewer side effects and reduced treatment-resistant potential. One of the options is to harness the anti-CRC potential of natural products. Previous studies have shown that Calamus draco exudate, dragon's blood, has anticancer activity in liver cancer and acute myeloid leukemia, but its bioactivity has not been studied in CRC. Here we conduct a bioinformatics study based on network pharmacology to explore the anti-CRC potential and mechanism of C. draco-derived compounds. The bioinformatics pipeline is composed of compound and target collection, biological network evaluation, and enrichment analysis. We found that there are 43 bioactive compounds from C. draco targeting 91 CRC-related targets, of which most compounds target MEN1, PTGS2, and IDH1. Further analyses show that the targets of C. draco are involved in the cellular response to hypoxia. By inhibiting those targets, C. draco bioactive compounds can potentially hinder angiogenesis and increase treatment response efficacy. © 2024 The Authors.

关键词： Lung cancer

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data Mining and bioinformatics Approaches to Elucidate Bacterial Communities in the Extreme Environment

Data Mining and Bioinformatics Approaches to Elucidate Bacte...

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International Conference on Informatics, Multimedia, Cyber and Information System (ICIMCIS)

作者： Joko Pebrianto Trinugroho Alam Ahmad Hidayat Rudi Nirwantono Faisal Asadi Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Mathematics Department School of Computer Science Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Biotechnology Department Faculty of Engineering Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Computer Science Department School of Computer Science Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program Master of Computer Science Bina Nusantara University Jakarta Indonesia

Bacteria are microscopic organisms that can be found in many environments. They are abundant and have many roles in our life. Studying bacteria is essential so that we can identify the bacteria that are needed for many industrial applications. However, the main problem is that majority of the bacteria are unculturable, hampering the exploration of bacteria from different environments. Metagenomics approach which employs Next Generation Sequencing technology could help study bacteria by utilizing 16S rRNA marker gene. This study aims to demonstrate data mining and bioinformatics approaches to analyze 16S rRNA sequencing data. The raw sequencing data of 16S rRNA was collected from biological database. Then, the data were trimmed, denoised, and clustered to generate Amplicon Sequence Variants (ASVs). Diversity (alpha and beta) and taxonomic analyses were then conducted to elucidate the bacterial diversity and taxonomic profile of ASVs. The results of this work showed that Shannon and PD indices in China's hot spring were higher than Singapore and the USA. Furthermore, a significant difference was observed in the PD index. The unweighted UniFrac distance also showed there was a significant difference of the bacterial communities between the three locations. In addition, the taxonomic investigation unveiled prevalent bacterial groups in the ecosystem, namely Proteobacteria, Chloroflexi, Cyanobacteria, and Crenarchaeota. The research outcomes have the potential to serve as a foundational resource for subsequent bacterial metagenomic research, particularly the hot spring environment.

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Novel loci and potential mechanisms of major depressive disorder,bipolar disorder,and schizophrenia

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Science China(Life Sciences) 2022年第1期65卷 167-183页

作者： He Wang Zhenghui Yi Tieliu Shi Center for Bioinformatics and Computational Biology Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China Shanghai Mental Health Center Shanghai Jiao Tong University School of MedicineShanghai 200030China Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal UniversityShanghai 200062China Beijing Advanced Innovation Center for Big Data-Based Precision Medicine Beihang University&Capital Medical UniversityBeijing 100083China

Different psychiatric disorders share genetic relationships and pleiotropic loci to certain *** integrated and analyzed datasets related to major depressive disorder(MDD),bipolar disorder(BIP),and schizophrenia(SCZ)from the Psychiatric Genomics Consortium using multitrait analysis of genome-wide association analysis(MTAG).MTAG significantly increased the effective sample size from 99,773 to 119,754 for MDD,from 909,061 to 1,450,972 for BIP,and from 856,677 to 940,613 for *** discovered 7,32,and 43 novel lead single nucleotide polymorphisms(SNPs)and 1,6,and 3 novel causal SNPs for MDD,BIP,and SCZ,respectively,after *** identified rs8039305 in the FURIN gene as a novel pleiotropic locus across the three *** performed marker analysis of genomic annotation(MAGMA)and Hi-C-coupled MAGMA(H-MAGMA)based gene-set analysis and identified 101 genes associated with the three disorders,which were enriched in the regulation of postsynaptic membranes,postsynaptic membrane dopaminergic synapses,and Notch signaling ***,we performed Mendelian randomization analysis using different tools and detected a causal effect of BIP on ***,we demonstrated the usage of combined genome-wide association studies summary statistics for exploring potential novel mechanisms of the three psychiatric disorders,providing an alternative approach to integrate publicly available summary data.

关键词： psychiatric disorders multitrait analysis of genome-wide association analysis novel loci Mendelian randomization causal effects

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